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- PDB-9op9: Two Component Protein Nano-Particle (T=3). De Novo Design, Comput... -

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Basic information

Entry
Database: PDB / ID: 9op9
TitleTwo Component Protein Nano-Particle (T=3). De Novo Design, Computationally Relaxed into Low Resolution Subtomogram Averaged CryoEM Map with Icosahedral Symmetry Applied
Components
  • C2-B
  • C3-A
KeywordsDE NOVO PROTEIN / Goldberg icosahedron / C60 / Fullerene
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 31.6 Å
AuthorsDiMaio, F. / Chmielewski, D. / Weidle, C.
Funding support United States, France, 8items
OrganizationGrant numberCountry
Defense Threat Reduction Agency (DTRA)HDTRA1-19-1-0003 United States
Burroughs Wellcome Fund United States
Human Frontier Science Program (HFSP)RGP0061/2019 France
Bill & Melinda Gates FoundationINV-043758 United States
Bill & Melinda Gates FoundationOPP1156262 United States
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute on Aging (NIH/NIA)R01AG063845 United States
Department of Energy (DOE, United States)KP1607011 United States
CitationJournal: Nature / Year: 2026
Title: De novo design of quasisymmetric two-component protein cages
Authors: Wang, S. / Xie, Y. / Chemielewski, D. / Weidle, C. / Hernandez, C. / Chen, W. / Ahn, G. / Duran, D.C. / Bera, A.K. / Bethel, N. / Decarreau, J. / Tong, S. / Kang, A. / Brackenbrough, E. / ...Authors: Wang, S. / Xie, Y. / Chemielewski, D. / Weidle, C. / Hernandez, C. / Chen, W. / Ahn, G. / Duran, D.C. / Bera, A.K. / Bethel, N. / Decarreau, J. / Tong, S. / Kang, A. / Brackenbrough, E. / Joyce, E. / Lee, S. / Wu, K. / Borst, A.J. / Favor, A. / Buwei, H. / DiMaio, F. / Holt, L. / Baker, D.
History
DepositionMay 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2026Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
ZA: C2-B
YC: C2-B
YD: C3-A
ZY: C2-B
ZZ: C3-A
YE: C2-B
YF: C3-A
YG: C2-B
YH: C3-A
YI: C2-B
YJ: C3-A
YK: C2-B
YL: C3-A
YM: C2-B
YN: C3-A
YO: C2-B
YP: C3-A
YQ: C2-B
YR: C3-A
YS: C2-B
YT: C3-A
YU: C2-B
YV: C3-A
AA: C2-B
AB: C3-A
YW: C2-B
YX: C3-A
ZB: C3-A
YY: C2-B
YZ: C3-A
AC: C2-B
AD: C3-A
AE: C2-B
AF: C3-A
AG: C2-B
AH: C3-A
AI: C2-B
AJ: C3-A
AK: C2-B
AL: C3-A
AM: C2-B
AN: C3-A
AO: C3-A
AP: C2-B
AQ: C3-A
AR: C2-B
AS: C2-B
AT: C3-A
AU: C2-B
AV: C3-A
AW: C2-B
AX: C3-A
AY: C2-B
AZ: C3-A
ZC: C2-B
BA: C2-B
BB: C3-A
BC: C2-B
BD: C3-A
BE: C2-B
BF: C3-A
BG: C2-B
BH: C3-A
BI: C2-B
BJ: C3-A
BK: C2-B
BL: C3-A
BM: C2-B
BN: C3-A
BO: C2-B
BP: C3-A
BQ: C2-B
BR: C3-A
BS: C2-B
BT: C3-A
BU: C2-B
BV: C3-A
BW: C2-B
BX: C3-A
BY: C2-B
BZ: C3-A
ZD: C3-A
CA: C2-B
CB: C3-A
CC: C2-B
CD: C3-A
CE: C2-B
CF: C3-A
CG: C2-B
CH: C3-A
CI: C2-B
CJ: C3-A
CK: C2-B
CL: C3-A
CM: C2-B
CN: C3-A
CO: C2-B
CP: C3-A
CQ: C2-B
CR: C3-A
CS: C2-B
CT: C3-A
CU: C2-B
CV: C3-A
CW: C2-B
CX: C3-A
CY: C2-B
CZ: C3-A
ZE: C2-B
DA: C2-B
DB: C3-A
DC: C2-B
DD: C3-A
DE: C2-B
DF: C3-A
DG: C2-B
DH: C3-A
DI: C2-B
DJ: C3-A
DK: C2-B
DL: C3-A
DM: C2-B
DN: C3-A
DO: C2-B
DP: C3-A
DQ: C2-B
DR: C3-A
DS: C2-B
DT: C3-A
DU: C2-B
DW: C3-A
DX: C2-B
DY: C3-A
DZ: C2-B
EA: C3-A
ZF: C3-A
EB: C2-B
EC: C3-A
ED: C2-B
EE: C3-A
EF: C2-B
EG: C3-A
EH: C2-B
EI: C3-A
EJ: C2-B
EK: C3-A
EL: C2-B
EM: C3-A
EN: C2-B
EO: C3-A
EP: C2-B
EQ: C3-A
ER: C2-B
ES: C3-A
ET: C2-B
EU: C3-A
EV: C2-B
EW: C3-A
EX: C2-B
EY: C3-A
EZ: C2-B
FA: C3-A
ZG: C2-B
FB: C2-B
FC: C3-A
FD: C2-B
FE: C3-A
FF: C2-B
FG: C3-A
FH: C2-B
FI: C3-A
FJ: C2-B
FK: C3-A
FL: C2-B
FM: C3-A
FN: C2-B
FO: C3-A
FP: C2-B
FQ: C3-A
FR: C2-B
FS: C3-A
FT: C2-B
FU: C3-A
FV: C2-B
FW: C3-A
FX: C2-B
FY: C3-A
FZ: C2-B
GA: C3-A
ZH: C3-A
GB: C2-B
GC: C3-A
GD: C2-B
GE: C3-A
GF: C2-B
GG: C3-A
GH: C2-B
GI: C3-A
GJ: C2-B
GK: C3-A
GL: C2-B
GM: C3-A
GN: C2-B
GO: C3-A
GP: C2-B
GQ: C3-A
GR: C2-B
GS: C3-A
GT: C2-B
GU: C3-A
GV: C2-B
GW: C3-A
GX: C2-B
GY: C3-A
GZ: C2-B
HA: C3-A
ZI: C2-B
HB: C2-B
HC: C3-A
HD: C2-B
HE: C3-A
HF: C3-A
WB: C2-B
HG: C2-B
HH: C3-A
HI: C2-B
HJ: C3-A
HK: C3-A
WA: C2-B
HL: C2-B
HM: C3-A
HN: C2-B
HO: C3-A
HP: C2-B
HQ: C3-A
HR: C2-B
HS: C3-A
HT: C2-B
HU: C3-A
HV: C2-B
HW: C3-A
HX: C2-B
HY: C3-A
HZ: C2-B
IA: C3-A
ZJ: C3-A
IB: C3-A
WC: C2-B
IC: C2-B
ID: C3-A
IE: C2-B
IF: C3-A
IG: C3-A
IH: C2-B
II: C2-B
IJ: C3-A
IK: C2-B
IL: C3-A
IM: C2-B
IN: C3-A
IO: C2-B
IP: C3-A
IQ: C2-B
IR: C3-A
IS: C2-B
IT: C3-A
IU: C2-B
IV: C3-A
IW: C2-B
IX: C3-A
IY: C2-B
IZ: C3-A
JA: C2-B
ZK: C2-B
JB: C3-A
JC: C2-B
JD: C3-A
JE: C2-B
JF: C3-A
JG: C2-B
JH: C3-A
JI: C2-B
JJ: C3-A
JK: C2-B
JL: C3-A
JM: C2-B
JN: C3-A
JO: C2-B
JP: C3-A
JQ: C2-B
JR: C3-A
JS: C2-B
JT: C3-A
JU: C3-A
WD: C2-B
JV: C2-B
JW: C3-A
JX: C2-B
JY: C3-A
JZ: C2-B
KA: C3-A
ZL: C3-A
KB: C2-B
KC: C3-A
KD: C2-B
KE: C3-A
KF: C2-B
KG: C3-A
KH: C2-B
KI: C3-A
KJ: C2-B
KK: C3-A
KL: C2-B
KM: C3-A
KN: C2-B
KO: C3-A
KP: C2-B
KQ: C3-A
KR: C2-B
KS: C3-A
KT: C2-B
KU: C3-A
KV: C2-B
KW: C3-A
KX: C2-B
KY: C3-A
KZ: C2-B
LA: C3-A
ZM: C2-B
LB: C2-B
LC: C3-A
LD: C2-B
LE: C3-A
LF: C2-B
LG: C3-A
LH: C2-B
LI: C3-A
LJ: C2-B
LK: C3-A
LL: C2-B
LM: C3-A
LN: C2-B
LO: C3-A
LP: C2-B
LQ: C3-A
LR: C2-B
LS: C3-A
ZN: C3-A
ZO: C2-B
ZP: C3-A
ZQ: C2-B
ZR: C3-A
ZS: C2-B
ZT: C3-A
ZU: C2-B
ZV: C3-A
ZW: C2-B
ZX: C3-A
YA: C2-B
YB: C3-A


Theoretical massNumber of molelcules
Total (without water)8,275,129360
Polymers8,275,129360
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
C2-B


Mass: 12591.434 Da / Num. of mol.: 180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21* (DE3)
#2: Protein ...
C3-A


Mass: 33381.504 Da / Num. of mol.: 180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21* (DE3)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Protein structure is equivalent to a C60 fullerene and has the general shape of a soccer ball with 12 pentagonal and 20 hexagonal facets. There are a total of 60 vertices (C3-A) and 90 edges (C2-B)
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain: BL21* (DE3)
Buffer solutionpH: 8 / Details: 25 mM Tris-HCl and 300 mM NaCl (pH 8)
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMtris(hydroxymethyl)aminomethane Hydrochloric AcidTris-HCl1
2300 mMSodium ChlorideNaCl1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 22000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 2.68 e/Å2 / Avg electron dose per subtomogram: 110 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4EMAN2CTF correction
7Rosettamodel fitting
9PHENIX1.21.2_5419model refinement
10cryoSPARCinitial Euler assignment
11EMAN2final Euler assignment
13EMAN23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 142674
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 31.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 462 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 462 / Num. of volumes extracted: 599
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingDetails: Computational Design / Source name: Other / Type: in silico model

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